Kyran Thompson's close-range finish fired Newcastle's second-string into an early lead at Victoria Park and despite Jack Nolan's header drawing Hartlepool level before the half-hour mark, Thompson's deflected effort restored United's advantage before the half-time break.
The young Magpies produced a resolute defensive display, restricting Pete Wild's side to zero shots on target in the second half, to record back-to-back wins in all competitions for the first time this season.
Robbie Stockdale made three changes from Friday's 4-1 win against Luton Town in the Premier League Cup as Mason Miley and Thompson, both named on the bench for the Magpies' Premier League win against Hull City last month, were handed starts while 16-year-old goalkeeper Roman Dowell replaced Aidan Harris in-between the sticks.
Hartlepool, situated in 20th place of the English fifth tier, struck the crossbar in the opening stages of the cup clash as Luke Charman, a former product of the Magpies' Academy, rose from Max Clark's inviting cross but the 28-year-old forward's close-range header cannoned off the woodwork before the loose ball was hacked clear to safety.
Newcastle took the lead in the ninth minute as Thompson scored his second goal in as many starts at Under-21 level. As Logan Watts' excellent diagonal pass found Johnny Emerson on the right flank, the Cumbrian winger directed a low cross into Thompson's path before the England Under-18 international placed a first-time effort beyond Hartlepool goalkeeper Nathan Fisher.
In front of 578 spectators, including 107 travelling away fans, the hosts aimed to draw themselves level as Jack Nolan cut inside from the right wing but the Pools winger's speculative drive from distance was comfortably held by Dowell.
Thompson went close to doubling his and Newcastle's tally as the London-born forward, who signed his first professional contract with the Magpies on his 17th birthday, raced onto Scott Bailey's lofted pass before his half-volley was pushed around the left-hand post in unorthodox fashion by Fisher.
Newcastle's youngsters found themselves on level terms in the 26th minute as Nolan arrived at the back post from Terry Bondo's in-swinging cross from the left wing before guiding a firm header into the bottom right-hand corner.
Matheos Ferreira, who made his senior debut for his boyhood club during July's pre-season friendly against Gateshead, missed a glorious chance to restore the visitors' lead after firing the ball over the bar from close-range following Emerson's teasing cutback from the byline.
In the 35th minute, however, Thompson regained Newcastle's one-goal cushion in fortunate circumstances as the promising teenager's goal bound strike from the edge of the box deflected off Pools skipper Reiss McNally before squirming through the gloves of Fisher.
Thompson, who joined the Magpies' youth set-up from Arsenal last summer, almost netted a first-half hat-trick after collecting Emerson's dangerous pass from the right flank inside the box but his resulting effort was dragged wide of the target.
In the second-half, Newcastle almost doubled their advantage from a dangerous counter-attack as Ferreira drove forward from inside his own half before finding Afner Cá but the Guinea-Bissau-born forward, who has scored three goals in his last five games at Under-21 level, saw his fierce strike blocked out for a corner.
Kyle Fitzgerald, introduced from the substitutes' bench, was unable to extend United's lead further in the closing stages as the Irish winger's cross-cum shot sailed wide of the left-hand post.
United's second-string held firm in the final stages to record maximum points in County Durham and now target a third victory in a row across all competitions when returning to Premier League 2 action on Monday, 26th October, hosting Sunderland at St. James' Park (kick-off 7pm GMT). Tickets are on sale here.
Newcastle United Under-21s: Roman Dowell, Henry Johnson, Dylan Charlton, Logan Watts, Miodrag Pivaš, Scott Bailey (c), Johnny Emerson (Alfie Seldon 63), Mason Miley, Afner Cá (Vakhtang Salia 77), Kyran Thompson (Kyle Fitzgerald 63), Matheos Ferreira (Jayden Kouossu 86).
Subs not used: Alexander Walpole, Luke Craggs, Guy Bloomer.
Photograph courtesy of Scott Llewellyn
